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Commit9df37a4

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committed
corrected factor column factorized and not reordering assigned events
1 parent2119c88 commit9df37a4

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4 files changed

+43
-5
lines changed

4 files changed

+43
-5
lines changed

‎R/Poisson_Regression.R‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -226,14 +226,14 @@ RunPoissonEventAssignment <- function(df, pyr0 = "pyr", event0 = "event", names
226226
}else {
227227
val_cols<- c(val_cols,col)
228228
}
229-
data.table::setkeyv(df0, c(pyr0,event0))
229+
# data.table::setkeyv(df0, c(pyr0, event0))
230230
}
231231
}else {
232232
df0<-data.table::data.table("a"= c(0,0))
233233
val<-list(cols= c("a"))
234234
val_cols<- c("a")
235235
}
236-
data.table::setkeyv(df, c(pyr0,event0))
236+
# data.table::setkeyv(df, c(pyr0, event0))
237237
all_names<- unique(names)
238238
df<- Replace_Missing(df,all_names,0.0,control$verbose)
239239
dfc<- match(names,all_names)
@@ -411,14 +411,14 @@ RunPoissonRegression_Residual <- function(df, pyr0 = "pyr", event0 = "event", na
411411
}else {
412412
val_cols<- c(val_cols,col)
413413
}
414-
data.table::setkeyv(df0, c(pyr0,event0))
414+
# data.table::setkeyv(df0, c(pyr0, event0))
415415
}
416416
}else {
417417
df0<-data.table::data.table("a"= c(0,0))
418418
val<-list(cols= c("a"))
419419
val_cols<- c("a")
420420
}
421-
data.table::setkeyv(df, c(pyr0,event0))
421+
# data.table::setkeyv(df, c(pyr0, event0))
422422
all_names<- unique(names)
423423
df<- Replace_Missing(df,all_names,0.0,control$verbose)
424424
dfc<- match(names,all_names)

‎R/SurvTypes.R‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -849,6 +849,11 @@ get_form_risk <- function(model_obj, df) {
849849
}
850850
}else {
851851
# it is a factor
852+
factor_arg_list<-list()
853+
factor_arg_list[[1]]<-element_col
854+
repeat_list<- c(list("_exp_type"="factor"), copy(factor_arg_list))
855+
repeat_list[["levels"]]<- levels(df[[element_col]])
856+
expres_calls[[length(expres_calls)+1]]<-repeat_list
852857
val<- factorize(df,element_col)
853858
df<-val$df
854859
col_name<-val$cols

‎tests/testthat/test-Assigned.R‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -35,7 +35,7 @@ test_that("Poisson Assigned Events, check results", {
3535

3636
e0<-e$predict
3737
e1<-e$caused
38-
38+
expect_equal(e1[,3],df$Cancer_Status,tolerance=1e-1)
3939
expect_equal(sum(e0),108.757,tolerance=1e-2)
4040
expect_equal(sum(e1),124,tolerance=1e-2)
4141

‎tests/testthat/test-Formula.R‎

Lines changed: 33 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -108,6 +108,17 @@ test_that("Basic generic function application to formula", {
108108
expect_no_error(f<- RelativeRisk(e,df))
109109
})
110110

111+
test_that("Basic factor application to formula with formula column", {
112+
df<- data.table("a"=1:100,"b"=2:101,"c"= c(rep(0,20), rep(1,80)),"d"= c(rep(1,20), rep(2,50), rep(3,30)),"e"=1:100)
113+
model<- Cox(a,b,c)~ loglinear(factor(d))
114+
expect_no_error(e<- CoxRun(model,df,ncores=2))
115+
expect_no_error(f<- RelativeRisk(e,df))
116+
df$d<-factor(df$d)
117+
model<- Cox(a,b,c)~ loglinear(d)
118+
expect_no_error(e<- CoxRun(model,df,ncores=2))
119+
expect_no_error(f<- RelativeRisk(e,df))
120+
})
121+
111122
test_that("Checking formula works with result modification", {
112123
fname<-"dose.csv"
113124
colTypes<- c("double","double","double","integer")
@@ -319,6 +330,28 @@ test_that("Colossus Surv Errors", {
319330
#
320331
})
321332

333+
test_that("Pois multi_surv nonerror", {
334+
fname<-"dose.csv"
335+
set.seed(3742)
336+
colTypes<- c("double","double","double","integer")
337+
df<- fread(fname,nThread= min(c(detectCores(),2)),data.table=TRUE,header=TRUE,colClasses=colTypes,verbose=FALSE,fill=TRUE)
338+
df$rand0<- floor(runif(nrow(df))*5)
339+
df$rand1<- floor(runif(nrow(df))*5)
340+
df$weight<-df$t1/100
341+
#
342+
time1<-"t0"
343+
time2<-"t1"
344+
event<-"lung"
345+
#
346+
expect_no_error(get_form(Pois_Strata(pyr=t1,event=lung,rand0,rand1)~ loglinear(dose),df))
347+
expect_no_error(get_form(Pois_Strata(t1,lung,rand0,rand1)~ loglinear(dose),df))
348+
#
349+
df$rand0<-factor(df$rand0)
350+
df$rand1<-factor(df$rand1)
351+
expect_no_error(get_form(Pois_Strata(t1,lung,rand0)~ loglinear(dose),df))
352+
expect_no_error(get_form(Pois_Strata(t1,lung,rand0,rand1)~ loglinear(dose),df))
353+
})
354+
322355
test_that("CaseCon Surv Errors", {
323356
fname<-"dose.csv"
324357
set.seed(3742)

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